'\" t
.TH samtools-reheader 1 "14 July 2025" "samtools-1.22.1" "Bioinformatics tools"
.SH NAME
samtools reheader \- replaces the header in the input file
.\"
.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
.\" Permission is hereby granted, free of charge, to any person obtaining a
.\" copy of this software and associated documentation files (the "Software"),
.\" to deal in the Software without restriction, including without limitation
.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
.\" and/or sell copies of the Software, and to permit persons to whom the
.\" Software is furnished to do so, subject to the following conditions:
.\"
.\" The above copyright notice and this permission notice shall be included in
.\" all copies or substantial portions of the Software.
.\"
.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
.\" DEALINGS IN THE SOFTWARE.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
.de EX

.  in +\\$1
.  nf
.  ft CR
..
.de EE
.  ft
.  fi
.  in

..
.
.SH SYNOPSIS
.PP
samtools reheader
.RB [ -iP ]
.RB [ -c
.IR CMD " | " in.header.sam ]
.I in.bam

.SH DESCRIPTION
.PP
Replace the header in
.I in.bam
with the header in
.IR in.header.sam .
This command is much faster than replacing the header with a
BAM\(->SAM\(->BAM conversion.

By default this command outputs the BAM or CRAM file to standard
output (stdout), but for CRAM format files it has the option to
perform an in-place edit, both reading and writing to the same file.
No validity checking is performed on the header, nor that it is suitable
to use with the sequence data itself.

.SH OPTIONS
.TP 8
.B -P, --no-PG
Do not add a @PG line to the header of the output file.
.TP 8
.B -i, --in-place
Perform the header edit in-place, if possible.  This only works on CRAM
files and only if there is sufficient room to store the new header.
The amount of space available will differ for each CRAM file.
.TP 8
.BI "-c, --command " CMD
Allow the header from 
.I in.bam
to be processed by external 
.I CMD
and read back the result. When used in this manner, the external header file
.I in.header.sam
has to be omitted.

.I CMD
must take the original header through stdin in SAM format and output the
modified header to stdout.
.I CMD
is passed to the system's command shell.
Care should be taken to ensure the command is quoted correctly to avoid unwanted
shell expansions (for example of $ variables).

.I CMD
must return an exit status of zero.

.SH EXAMPLES

.IP \(bu 2
Remove comment lines
.EX 2
samtools reheader -c 'grep -v ^@CO' in.bam
.EE
.IP \(bu 2
Add \(lqChr\(rq prefix to chromosome names.  Note extra backslashes before
dollar signs to prevent unwanted shell variable expansion.
.EX 2
samtools reheader -c 'perl -pe "s/^(@SQ.*)(\(rstSN:)(\(rsd+|X|Y|MT)(\(rss|\(rs$)/\(rs$1Chr\(rs$2\(rs$3/"' in.bam
.EE
.IP \(bu 2
Remove \(lqChr\(rq prefix
.EX 2
samtools reheader -c 'perl -pe "s/^(@SQ.*)(\(rstSN:)Chr/\(rs$1\(rs$2/"' in.bam
.EE

.SH AUTHOR
.PP
Written by Heng Li with modifications by James Bonfield and Valeriu Ohan,
all from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
